In this study we investigated genetic variation in three populations of elephant seals, two of the southern species (Mirounga leonina) and one of the northern species (M. angustirostris). These two species are very closely related. The northern species was hunted nearly to extinction in the last century, and has since recovered to over 100,000 seals. We investigated the extent of the bottleneck using a simulation model approach, determined life history parameters using hypervariable DNA markers, and assessed the level of post-bottleneck variation in several molecular and quantitative genetic characters. The simulation model indicated a very small bottleneck population size of 10-30 seals (95% confidence limits). Paternity testing using DNA fingerprinting and microsatellite DNA analysis indicated low levels of effective polygyny in the northern species, despite behavior indicating strong polygyny in most harems. This may suggest a reduction in male fertility in this species, perhaps, as a result of the population bottleneck. Genetic analyses indicated reduced molecular genetic variation in mitochondrial DNA, microsatellite DNA, minisatellite DNA and major histocompatibility complex class II genes. Variation at several quantitative characters increased, or became more asymmetrical following the bottleneck. These results permit a detailed analysis of the effects of inbreeding on genetic variation in a natural population, and provide insight into the ways in which variation accumulates and is maintained.